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Figure 1 | BMC Genomics

Figure 1

From: Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array

Figure 1

This figure summarises the comparison between WGBS and HM450K beta-values for the H1-hESC cell line. Figures a) and b) show contour plots demonstrating the correlation of DNA methylation between WGBS and HM450K bead array for Infinium I probes and Infinium II probes respectively. The contours (different colour intensities) capture the density of beta-values. It can be seen that most points reside close to 0, 0 and 1, 1, resulting in high-correlation between the platforms. Figures c) and d) show boxplots of DNA methylation results (absolute beta differences) between WGBS and HM450K bead array, plotted for different potential filtering categories for Infinium I and II probes respectively. The box extends from the first to the third quartile and whiskers extend to 1.5 times the interquartile range. Points outside this are considered outliers. The blue boxplots show the distribution of filtering category probes that were statistically significantly different from the high quality probes (golden boxplot) (P < 0.001) otherwise, the category is plotted as light green. The red dotted line depicts the median of a high quality probe set. Category definitions: High-quality - represents probes which are not affected by any genomic factors; Repeats - describes probes which hybridize to repetitive regions; Bis-okay – are probes which hybridize regions containing any C– > T SNP or T- > C SNP and are ‘okay’ in bisulfite space; SNP-at-CpG-C and SNP-at-CpG-G - are probes which have SNPs at the interrogated C and its neighbouring G position, respectively; Indels - are probes which hybridize regions containing INDELs; Multimap - are probes which hybridize to multiple genomic loci; SNP-1 - are probes which contain only a single SNP anywhere in the body; and SNP > = 2 - are probes which contain at least 2 SNPs anywhere in the probe body.

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